Abstract 3610: In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer
Authors: Juan Dubrot, Peter P. Du, Sarah Kate Lane-Reticker, Emily A. Kessler, Audrey J. Muscato, Arnav Mehta, Samuel S. Freeman, Peter M. Allen, Kira E. Olander, Kyle M. Ockerman, Clara H. Wolfe, Fabius Wiesmann, Nelson H. Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M. Schneider, Andrea N. Rivera-Rosario, Ian C. Kohnle, Hans W. Pope, Austin Ayer, Gargi Mishra, Margaret D. Zimmer, Sarah Y. Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T. Frederick, Genevieve M. Boland, W. Nicholas Haining, David E. Root, John G. Doench, Nir Hacohen, Kathleen B. Yates, Robert T. Manguso
Journal: Cancer Research (2022)

Abstract The immune system can eliminate tumors, but checkpoints enable tumors to escape immune destruction. Here, we report the systematic identification of immune evasion mechanisms using genome-scale in vivo CRISPR screens in eight murine cancer models treated with immune checkpoint blockade (ICB). We identify and validate previously unreported immune evasion genes and identify key immune inhibitory checkpoints that have a conserved role across several cancer models, such as the non-classical MHC-I molecule Qa-1b/HLA-E, which scores as the top overall sensitizing hit across all screens. Surprisingly, we find that loss of IFNγ signaling by tumor cells sensitizes 6 of 8 cancer models to ICB. While IFN-mediated inflammation has been associated with response to ICB, there have also been reports of ICB-resistance driven by IFN sensing. However, several divergent mechanisms have been proposed to explain the inhibitory effect of tumor IFN sensing, leading to uncertainty about how this key immune signaling pathway is regulating anti-tumor immunity in different contexts. Using in vivo screening data, transcriptional profiling, and genetic interaction studies, we reveal that the immune-inhibitory effects of tumor IFN sensing are the direct result of tumor upregulation of classical and non-classical MHC-I genes. The interferon-MHC-I axis can inhibit anti-tumor immunity through two mechanisms: first, upregulation of classical MHC-I inhibits the cytotoxicity of natural killer cells, which are activated by ICB. Second, IFN-mediated upregulation of Qa-1b directly inhibits cytotoxicity by effector CD8+ T cells via the NKG2A/CD94 receptor, which is induced on CD8+ T cells by ICB. Finally, we show that high interferon-stimulated gene expression in patients is associated with decreased survival in RCC and poor response to ICB in melanoma. Our study establishes a unifying mechanism to explain the inhibitory role of tumor IFN sensing, revealing that IFN-mediated upregulation of classical and non-classical MHC-I inhibitory checkpoints can facilitate immune escape. Citation Format: Juan Dubrot, Peter P. Du, Sarah Kate Lane-Reticker, Emily A. Kessler, Audrey J. Muscato, Arnav Mehta, Samuel S. Freeman, Peter M. Allen, Kira E. Olander, Kyle M. Ockerman, Clara H. Wolfe, Fabius Wiesmann, Nelson H. Knudsen, Hsiao-Wei Tsao, Arvin Iracheta-Vellve, Emily M. Schneider, Andrea N. Rivera-Rosario, Ian C. Kohnle, Hans W. Pope, Austin Ayer, Gargi Mishra, Margaret D. Zimmer, Sarah Y. Kim, Animesh Mahapatra, Hakimeh Ebrahimi-Nik, Dennie T. Frederick, Genevieve M. Boland, W. Nicholas Haining, David E. Root, John G. Doench, Nir Hacohen, Kathleen B. Yates, Robert T. Manguso. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3610.